Emilysimso Week 15

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Procedure

  • Calculated averages from split data for each time point and replicate
    • Total of 5409 genes
  • Calculated biological averages of each time point
  • Calculated AverageLogRatio comparing C5, C20, and C60 to C0 and F5, F20, and F60 to C60
    • Subtracted not divided due to log space
  • Performed TTest on the above relationships to get the Pvalue
  • Performed Bonferroni
  • Performed Benjamini & Hochberg
  • Created new sheet forGenMAPP
    • Did adjustments to prepare file for GenMAPP
    • Saved as .txt and uploaded to wiki

GenMAPP

  • Increase criterea = >0.25 AND B-H <0.05
  • Decrease criterea <-0.25 AND B-H <0.05
  • 1441 errors in the raw data
  • Red is increased, green is decreased
  • Uploaded C5-C0, C20-C0, C60-C0, F5-C60, F20-C60, and F60-C60 into GenMAPP

MAPPFinder

  • Criteria: Zscore >2, Permute P<0.05, Number Changed > or equal to 4 < or equal to 100, Percent Changed > or equal to 50%

Files

Individual Reflection

Statement of Work

I was a GenMAPP User for the group project, meaning I did the raw data analysis from the microarray experiment and worked with the program to analyze the results. I compiled the data from the repletion stage of the experiment (all of the F time points - found on my Week 12 page) and then combined this data with Ron to perform the statistical analysis on the data (found on my Week 14 page). I also created the file we used for GenMAPP. I worked with Josh to enter the data into GenMAPP and then worked with Ron to figure out the criteria for significance of the increased and decreased genes. I also created the MAPPs for the Fatty Acid Degradation and Ribosome gene pathways, as well as the compiled Fatty Acid Degradation and Ribosome pathways. Finally, I created the experimental design flow chart.

I also wrote the vast majority of the paper, compiled all of the tables and figures, and led the group for this portion.

Assessment of Project

I think our group worked fairly well together, but we had some issues with communication. Everyone was responsible and got their work done, but sometimes it was unclear when things would be finished or who needed to do which task. There were also some problems with direction and we could have used someone taking a stronger leadership role. I think we should have met more together outside of class to clear up some of these issues, so I would have definitely done that differently. Specifically, Ron and I should have met more to work on the Excel files, since it was unnecessarily complicated doing it apart from each other. Overall, however, I think our group was able to work together to finish the project.

Our Gene Database Project was mostly complete, however, we were missing the compiled MAPPFinder files for the Ribosome and Fatty Acid Degradation pathways. We also could have done a more thorough comparison between our results and the Yang et al. microarray data. I think our overall quality was fairly high and our organization worked well. Our Group Paper was more complete than the presentation because we added the elements initially missing. I think we could have gone further in our analysis, but the rest of the group thought that might be unnecessary.

Reflection on the Process

I learned a lot from this project and I think the class as a whole will stay with me beyond undergrad. This course helped solidify the connection between biology and computer science, which is something I had not previously thought much about. I think I learned more about computer science overall, as I had not been exposed to that field before, in terms of database construction, coding, and how various programs can be put together for a final result. In terms of teamwork, this project reminded me how important it is to use people’s skills and work together to make the best project. This project was very specialized, so building off of individual knowledge definitely helped. I think this will help with future projects, especially as they become more involved and specific. I was also reminded about my own leadership style and group role. For technical skills, I learned how to do some basic coding, database construction, and analysis of a species’ genome. Learning to interpret genomic data is an important skill to start building, as the field is always growing and becoming increasingly relevant to biology.

The biggest lesson I will take away is that even if a project seems daunting, it can be tackled; before coming into this course, I knew very little about computer science and databases, so having a finished product is very rewarding.


Weekly Assignment Information

User: Emilysimso

Assignments

Individual Journal Entries

Class Journal Entries

Group Project

Heavy Metal HaterZ

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